Re: Question about the fundamentals of MD and WHAM

From: Giacomo Fiorin (
Date: Fri Jul 20 2018 - 07:42:40 CDT

These fundamental questions are best covered by textbooks:
"Introduction to modern statistical mechanics" (David Chandler)
"Understanding Molecular Simulation: From Algorithms to Applications" (Daan
Frenkel and Berend Smit)
"Free Energy Calculations: Theory and Applications in Chemistry and Biology"
(Cristophe Chipot and Andrew Pohorille)
"Statistical Mechanics: Theory and Molecular Simulation" (Mark Tuckerman)

This is not a complete list, but should get you started. You should also
search the mailing list archives for this or other MD codes, because this
question is recurring.

On Thu, Jul 19, 2018 at 4:54 PM Junwoong Yoon <>

> Dear NAMD users,
> I am a beginner in NAMD. I have several questions about the fundamentals
> of MD and WHAM. These might be trivial to you but I really want to
> understand how MD and WHAM work beforehand. I already did some research to
> answer these questions but it was a bit difficult to fully understand as a
> beginner...
> 1) I want to know what does MD actually do when the colvar is off (no
> external potentials) and on. Does it just determine what is the equilibrium
> (lowest energy) state when colvar is off?
> 2) I heard that it often takes too long to find the full free energy
> landscape without external bias potentials. If this is because of lack of
> sampling beyond the energy barriers, what actually hinders the sampling (or
> how the probability came from)? And how the low probability to sample
> beyond the barrier is related to thermodynamic quantities such as free
> energy, etc?
> 3) When we apply external bias potentials using Umbrella Sampling methods,
> how will WHAM unbias them? I saw some equations that explains how it works
> but could not fully understood.
> I really appreciate your taking time to help others.
> Best,
> Jun

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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